Based at the Pacific School of Religion, they host various events for Christian clergy and people of faith, and their website has a variety of downloadable PDFs for creating community, and to spur conversation.
http://clgs.org/

A resource of the National LGBTQ Task Force, they help Christian and Jewish people find welcoming congregations or seminary programs, offer trainings and events, and have a variety of downloadable resources.
http://www.welcomingresources.org/

This open-source project, though academic in nature, is accessible and has information on trans and gender nonconforming experience across faith and spirituality perspectives across history, from atheism and Christianity to Hinduism and Wicca and beyond.
http://www.transtheology.org/